chr9-111943865-T-C

Variant names:

• chr9-111943865-T-C
• rs7863587
• XR_007061735.1:n.1093A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061735.1(LOC124902250):​n.1093A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,166 control chromosomes in the GnomAD database, including 1,886 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (1886 hom., cov: 32)
• Consequence: LOC124902250 XR_007061735.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 5 publications found

Genes affected

LOC124902250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23603 AN: 152048 Hom.: 1877 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.155 AC: 23643 AN: 152166 Hom.: 1886 Cov.: 32 AF XY: 0.155 AC XY: 11506 AN XY: 74392

African (AFR) AF: 0.165 AC: 6831 AN: 41490

American (AMR) AF: 0.112 AC: 1707 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3466

East Asian (EAS) AF: 0.0929 AC: 481 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1218 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1635 AN: 10594

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10734 AN: 68012

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.163 Hom.: 1166

Bravo AF: 0.150

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.31
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7863587; hg19: chr9-114706145;